DOCK GA Development Goals
| Tasks | src | Owner | Complete? |
|---|---|---|---|
| Fix bug that collapsed atom coordinates | everywhere? nowhere? | everyone | No |
| Added Delimeter header | conf_gen_ga | LEP | Yes |
| Fix xover only feature | conf_gen_ga | LEP | No |
| Put in error messages for mut_rate > 1 | conf_gen_ga | LEP | Yes |
| Manual user-defined mutation type | conf_gen_ga | LEP | No |
To Do List
-xover- -guided based on score 1. good v good 2. bad v good 3. bad v bad -nonexhaustive xover (pick subset of xover based on probability) -2-3 point xover at once -adaptive maintenance ensemble based on ensemble convergence -bring in new parents based on convergence -Mutations- -adaptive mutation rate -pick location of mutation based on something -pick mutation type based on behavior of esemble too large boost deletion too small more add change ...boost replace/sub -mutation type selection based on probability vs ensemble -complete x # y mutation so far so less prevalent etc -3 layer subs do no work so don't do them -replace > 1 segment -fitness- -turn on and off niching adaptive/extinction -reduce boost of fragments and all poor mols with niching -pareto/mulitobjective ga -selection- -metropolis selection for tournament/roulette -adaptive keep #p and #o -extinction- -automated vs on convergence -stop- -convergence -which molecules are best- -best first pruning - now uses descriptor score even if niching ned to delta to fitness/niching when used
